Tests of selection indicated that integrated genes are maintained by purifying selection.
If these were maintained by purifying selection then U-rich SREs would be uniformly distributed throughout the genome.
Altogether, our data indicate that SSQ1 was subjected to divergent evolution driven by lowered expression levels and functional diversification, but that critical function was maintained by purifying selection.
Both molecular evolution and population genetics support the hypothesis that conservation of miRNA binding sites is maintained by purifying selection through elimination of deleterious alleles.
Overall our results reveal that the three ribosomal protein S13 genes in Malus are undergoing higher purifying selection than neutral evolution, suggesting that their functionality is maintained by purifying selection.
Furthermore, protein function is maintained by purifying selection against internal changes that may disrupt enzyme function, restricting positive selection to amino acids exposed to the surface of the protein's three dimensional structure [ 50].
These observations raise the question whether the HR pathway in general and functional redundancy in this pathway in particular are maintained by purifying selection in Wolbachia because they are essential, or HR happens to take place merely because the pathway has not been pseudogenized yet.
The dN/dS ratio of the DUXA C-terminal domain (after HD2) in a pairwise comparison of human, chimpanzee, macaque and orangutan shows an average across all pairs that is below 1 (0.27), indicating that the newly gained sequence has been maintained by purifying selection.
The present study of within-species nucleotide variation of both the L and M opsin genes in gibbons provides additional support to previous studies suggesting that the gene conversion has homogenized the tandemly duplicated L and M opsin genes and their spectral difference is maintained by purifying selection on centrally-located exons in non-human catarrhines [ 13, 14, 26- 29].
Given the CpG → TpG/CpA mutation rate is about one order of magnitude higher than the reverse (Duncan and Miller 1980; Bulmer 1986; Sved and Bird 1990), 1) neutrally evolving codons will move toward a lower frequency of CpG; 2) CpG's at functionally significant codons will be maintained by substantial purifying selection against amino acid changes.
